Re: [galaxy-dev] How to set java heap size in Galaxy?
Hi Roman, Thanks for your explanation. I'm sorry for this late reply. I think the problem is on my app. I'll further check that. Thanks, Bo Date: Thu, 30 Jun 2011 14:53:08 +0200 From: Roman Valls To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How to set java heap size in Galaxy? Message-ID: <4e0c71b4.2010...@nopcode.org> Content-Type: text/plain; charset=ISO-8859-1 Hello Liu, I'm keeping our mail thread in the mailing list, as advised by its guidelines on the footer of each mail. Now, galaxy runs on top of paster, a minimal python webserver, but it has nothing to do with Java, looks like your out of memory error comes from your app then. Have you tried the suggested settings from Marco ? Namely: java -Xmx512m I bet there's an environment variable or config setting for Tomcat too if you're unsure about where your jar's are called. Hope that helps ! Roman On 2011-06-29 12:02, liu bo wrote: > Thank you, Roman. > Our app invoke a workflow server. > I guess Galaxy has a self container like Tomcat, that is why we can > access it via 127.0.0.1 from browser. > I know in Tomcat, there is a file "catalina.sh" for setting JAVA_OPTS. > Is there a similiar file in Galaxy to set JAVA_OPTS? > Thank you very much. > > Regards, > Bo > > On Tue, Jun 28, 2011 at 4:18 AM, Roman Valls wrote: >> Hi Liu, >> >> Does your app execute Picard/GATK at some point ? In that case those >> would be the ones triggering your Java OOM error, in that case Bo's >> suggestion is the way to go. That's my best guess since Galaxy itself >> doesn't use java either (only python AFAIK). >> >> Regards, >> Roman >> >> On 2011-06-27 18:44, liu bo wrote: >>> Hi Marco, >>> >>> Thanks for your kind reply. >>> My app is a python file, and there's not an explicit command to run java. >>> I just wonder whether there is a file to configure Galaxy, in order to >>> set the Java heap size. >>> Thank you. >>> >>> Best wishes, >>> Bo >>> >>> On Mon, Jun 27, 2011 at 7:51 PM, Marco Moretto >>> wrote: >>>> Hi Liu, >>>> if you set up your application in the XML to run with Java, like java -jar >>>> yourapplication.jar, it is sufficient to add the -Xmx parameter. Something >>>> like >>>> java -Xmx512m -jar yourapplication.jar >>>> Greets >>>> --- >>>> Marco >>>> >>>> >>>> On 27 June 2011 12:15, liu bo wrote: >>>>> >>>>> Dear all, >>>>> >>>>> I have added an application to Galaxy's Tools. >>>>> Now there occurs an error "java.lang.OutOfMemoryError: Java heap space". >>>>> Do you know how to set java heap size in Galaxy? >>>>> Thank you very much. >>>>> >>>>> Best regards, >>>>> Bo >>>>> ___ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> >>>>> http://lists.bx.psu.edu/ >>>> >>>> >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to set java heap size in Galaxy?
Hello Liu, I'm keeping our mail thread in the mailing list, as advised by its guidelines on the footer of each mail. Now, galaxy runs on top of paster, a minimal python webserver, but it has nothing to do with Java, looks like your out of memory error comes from your app then. Have you tried the suggested settings from Marco ? Namely: java -Xmx512m I bet there's an environment variable or config setting for Tomcat too if you're unsure about where your jar's are called. Hope that helps ! Roman On 2011-06-29 12:02, liu bo wrote: > Thank you, Roman. > Our app invoke a workflow server. > I guess Galaxy has a self container like Tomcat, that is why we can > access it via 127.0.0.1 from browser. > I know in Tomcat, there is a file "catalina.sh" for setting JAVA_OPTS. > Is there a similiar file in Galaxy to set JAVA_OPTS? > Thank you very much. > > Regards, > Bo > > On Tue, Jun 28, 2011 at 4:18 AM, Roman Valls wrote: >> Hi Liu, >> >> Does your app execute Picard/GATK at some point ? In that case those >> would be the ones triggering your Java OOM error, in that case Bo's >> suggestion is the way to go. That's my best guess since Galaxy itself >> doesn't use java either (only python AFAIK). >> >> Regards, >> Roman >> >> On 2011-06-27 18:44, liu bo wrote: >>> Hi Marco, >>> >>> Thanks for your kind reply. >>> My app is a python file, and there's not an explicit command to run java. >>> I just wonder whether there is a file to configure Galaxy, in order to >>> set the Java heap size. >>> Thank you. >>> >>> Best wishes, >>> Bo >>> >>> On Mon, Jun 27, 2011 at 7:51 PM, Marco Moretto >>> wrote: Hi Liu, if you set up your application in the XML to run with Java, like java -jar yourapplication.jar, it is sufficient to add the -Xmx parameter. Something like java -Xmx512m -jar yourapplication.jar Greets --- Marco On 27 June 2011 12:15, liu bo wrote: > > Dear all, > > I have added an application to Galaxy's Tools. > Now there occurs an error "java.lang.OutOfMemoryError: Java heap space". > Do you know how to set java heap size in Galaxy? > Thank you very much. > > Best regards, > Bo > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to set java heap size in Galaxy?
Hi Liu, Does your app execute Picard/GATK at some point ? In that case those would be the ones triggering your Java OOM error, in that case Bo's suggestion is the way to go. That's my best guess since Galaxy itself doesn't use java either (only python AFAIK). Regards, Roman On 2011-06-27 18:44, liu bo wrote: > Hi Marco, > > Thanks for your kind reply. > My app is a python file, and there's not an explicit command to run java. > I just wonder whether there is a file to configure Galaxy, in order to > set the Java heap size. > Thank you. > > Best wishes, > Bo > > On Mon, Jun 27, 2011 at 7:51 PM, Marco Moretto > wrote: >> Hi Liu, >> if you set up your application in the XML to run with Java, like java -jar >> yourapplication.jar, it is sufficient to add the -Xmx parameter. Something >> like >> java -Xmx512m -jar yourapplication.jar >> Greets >> --- >> Marco >> >> >> On 27 June 2011 12:15, liu bo wrote: >>> >>> Dear all, >>> >>> I have added an application to Galaxy's Tools. >>> Now there occurs an error "java.lang.OutOfMemoryError: Java heap space". >>> Do you know how to set java heap size in Galaxy? >>> Thank you very much. >>> >>> Best regards, >>> Bo >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to set java heap size in Galaxy?
Hi Marco, Thanks for your kind reply. My app is a python file, and there's not an explicit command to run java. I just wonder whether there is a file to configure Galaxy, in order to set the Java heap size. Thank you. Best wishes, Bo On Mon, Jun 27, 2011 at 7:51 PM, Marco Moretto wrote: > Hi Liu, > if you set up your application in the XML to run with Java, like java -jar > yourapplication.jar, it is sufficient to add the -Xmx parameter. Something > like > java -Xmx512m -jar yourapplication.jar > Greets > --- > Marco > > > On 27 June 2011 12:15, liu bo wrote: >> >> Dear all, >> >> I have added an application to Galaxy's Tools. >> Now there occurs an error "java.lang.OutOfMemoryError: Java heap space". >> Do you know how to set java heap size in Galaxy? >> Thank you very much. >> >> Best regards, >> Bo >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to set java heap size in Galaxy?
Hi Liu, if you set up your application in the XML to run with Java, like java -jar yourapplication.jar, it is sufficient to add the -Xmx parameter. Something like java -Xmx512m -jar yourapplication.jar Greets --- Marco On 27 June 2011 12:15, liu bo wrote: > Dear all, > > I have added an application to Galaxy's Tools. > Now there occurs an error "java.lang.OutOfMemoryError: Java heap space". > Do you know how to set java heap size in Galaxy? > Thank you very much. > > Best regards, > Bo > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] How to set java heap size in Galaxy?
Dear all, I have added an application to Galaxy's Tools. Now there occurs an error "java.lang.OutOfMemoryError: Java heap space". Do you know how to set java heap size in Galaxy? Thank you very much. Best regards, Bo ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
